organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890

rac-4,8-Di­vinyl­bi­cyclo­[3.3.1]nonane-2,6-dione

aDepartment of Organic Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania, and bOrganic Chemistry, Department of Chemistry, Lund University, PO Box 124, S-221 00 Lund, Sweden
*Correspondence e-mail: Carl-Johan.wallentin@organic.lu.se

(Received 7 May 2009; accepted 15 May 2009; online 20 May 2009)

The title compound, C13H16O2, is a chiral bicyclic structure composed of two fused cyclo­hexa­ne rings possessing both boat and chair conformations. The mol­ecules are packed in enantio­pure columns which are pairwise linked forming an overall racemic solid; within the column pairs the packing is governed by weak dipole–dipole inter­actions stemming from stacked carbonyl functionalities (COcentroid–COcentroid distance = 3.290 Å).

Related literature

For related structures, see: Orentas et al. (2007[Orentas, E., Bagdziunas, G., Berg, U., Zilinskas, A. & Butkus, E. (2007). Eur. J. Org. Chem. pp. 4251-4256.]); Quast et al. (1994[Quast, H., Becker, C., Geibler, E., Knoll, K., Peters, E.-M., Peters, K. & von Schnering, H. G. (1994). Liebigs Ann. Chem. pp. 109-120.], 1999[Quast, H., Seefelder, M., Peters, E.-M. & Peters, K. (1999). Eur. J. Org. Chem. pp. 1811-1823.]); Wallentin et al. (2009[Wallentin, C.-J., Orentas, E., Johnson, M. T., Butkus, E., Wendt, O. F., Öhrström, L. & Wärnmark, K. (2009). CrystEngComm. Submitted.]). For a general background to non-covalent inter­actions, see: Desiraju & Steiner (1999[Desiraju, G. R. & Steiner, T. (1999). In The Weak Hydrogen Bond. New York: Oxford University Press Inc.]); Aakeröy (1997[Aakeröy, C. B. (1997). Acta Cryst. B53, 569-586.]), and references therein.

[Scheme 1]

Experimental

Crystal data
  • C13H16O2

  • Mr = 204.26

  • Orthorhombic, P n a 21

  • a = 20.4254 (11) Å

  • b = 8.8913 (6) Å

  • c = 6.2570 (4) Å

  • V = 1136.32 (12) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.08 mm−1

  • T = 293 K

  • 0.3 × 0.05 × 0.03 mm

Data collection
  • Oxford Diffraction Xcalibur diffractometer

  • Absorption correction: multi-scan (CrysAlis RED; Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) Tmin = 0.827, Tmax = 1.000 (expected range = 0.825–0.998)

  • 8068 measured reflections

  • 1363 independent reflections

  • 811 reflections with I > 2σ(I)

  • Rint = 0.031

Refinement
  • R[F2 > 2σ(F2)] = 0.044

  • wR(F2) = 0.110

  • S = 1.02

  • 1363 reflections

  • 136 parameters

  • 1 restraint

  • H-atom parameters constrained

  • Δρmax = 0.32 e Å−3

  • Δρmin = −0.19 e Å−3

Data collection: CrysAlis CCD (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); cell refinement: CrysAlis RED (Oxford Diffraction, 2006[Oxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]); data reduction: CrysAlis RED; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: DIAMOND (Brandenburg, 2000[Brandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany.]); software used to prepare material for publication: WinGX (Farrugia, 1999[Farrugia, L. J. (1999). J. Appl. Cryst. 32, 837-838.]).

Supporting information


Comment top

The hydrocarbon backbone of the title compound is a common motif in many biologically active compounds and its unique molecular shape has been utilized in the construction of different types of supramolecular architectures and inclusion complexes. Diols from this category of structures has with great success been exploited within the field of crystal engineering. The title compound was obtained in the synthesis of a series of C2 -symmetrically derivatized bicyclo[3.3.1]nonane-2,6-diones as a part of an ongoing project with the aim to study various supramolecular features of this class of compounds. The chiral bicyclic structure is composed of two merged cyclohexanes possessing both boat and chair conformations similar to the previously reported phenyl-substituted bicyclo[3.3.1]nonane-2,6-dione (Quast et al., 1999). The molecules are packed in column pairs which propagate in a unidirectional manner along the c axis. The column pairs are homochiral and generated by a two fold screw axis. The glide plane generates an over-all racemic structure comprised of parallel columns with alternating absolute stereochemistry. The formation of column pairs is governed by dipole-dipole interactions stemming from stacked carbonyl functionalities: centroid C2O1···centroid C2O1, 3.290 Å.

Related literature top

For related structures, see: Orentas et al. (2007); Quast et al. (1994, 1999); Wallentin et al. (2009). For a general background to non-covalent interactions, see: Desiraju & Steiner (1999); Aakeröy (1997), and references therein.

Experimental top

A solution of LiCl in THF ( 0.5M, 12.5 mL, 6.25 mmol) was added to a round-bottom flask charged with CuCN (0.272 g, 3.04 mmol) and the mixture was stirred under argon at room temperature until all solid dissolved. The solution was cooled down to -30 °C and a solution of vinyl magnesium bromide in THF (0.7 M, 4.34 mL, 3.04 mmol) was added dropwise. The resulting dark brown mixture was warmed to -20 °C and stirred at this temperature for 30 minutes and then cooled to -78 °C. A solution of bicyclo[3.3.1]nona-3,7-diene-2,6-dione (0.15g, 1.01 mmol) (Orentas et al., 2007) and trimethylsilylchloride (0.33 g, 3.04 mmol) in THF (3 mL) was added dropwise. The reaction mixture was stirred until the temperature reached -20 °C. The reaction was quenched with 10% HCl solution (20 mL) and stirred at room temperature until the intermediate silylenol ether was hydrolyzed (monitored by TLC). The mixture was diluted with water and extracted with EtOAc (3 x 20 mL). The combined organic phase was dried over Na2SO4 and evaporated to dryness. The residue was purified by flash chromatography (10% ethyl acetate/petroleum ether) to afford the title compound as a coluorless solid in 70 % yield (144.4 mg). The product was recrystallised from petroleum ether to give colourless crystals suitable for X-ray diffraction analysis; m.p. 65 °C; FTIR (KBr) 1700 (C=O) cm-1; 1H NMR (300 MHz, CDCl3) δ 5.83 (ddd, J1=17.0 Hz, J2=10.4 Hz, J3=6.0 Hz, 1H), 5.17 (dd, J1=10.4 Hz, J2=1.6 Hz, 1H), 5.10 (dd, J1=17.0 Hz,J2=1.6 Hz, 1H), 2.93-2.83 (m, 2H), 2.62-2.53 (m, 6H), 2.19-2.14 (m, 2H); 13C NMR (75 MHz, CDCl3) δ 211.86, 139.34, 116.01, 48.10, 39.46, 22.81; Anal. calcd for C13H16O2: C, 76.44; H, 7.90. Found: C, 76.57; H, 8.02.

Refinement top

The H atoms were positioned geometrically and treated as riding on their parent atoms with C–H distances of 0.93–0.97 Å and Uiso(H) = 1.2Ueq - 1.5Ueq. Equivalent reflections including Friedel pairs were merged prior to the final refinement.

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: DIAMOND (Brandenburg, 2000); software used to prepare material for publication: WinGX (Farrugia, 1999).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound with atom labels and 30% probability displacement ellipsoids.
[Figure 2] Fig. 2. A partial packing diagram of the title compound displaying the weak interactions that govern the formation of column pairs. Dipol-dipol interactions are visualized as yellow lines connecting the carbonyl O atoms.
rac-4,8-Divinylbicyclo[3.3.1]nonane-2,6-dione top
Crystal data top
C13H16O2F(000) = 440
Mr = 204.26Dx = 1.194 Mg m3
Orthorhombic, Pna21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2c -2nCell parameters from 2363 reflections
a = 20.4254 (11) Åθ = 2.3–33.1°
b = 8.8913 (6) ŵ = 0.08 mm1
c = 6.2570 (4) ÅT = 293 K
V = 1136.32 (12) Å3Prism, colourless
Z = 40.3 × 0.05 × 0.03 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer
1363 independent reflections
Radiation source: Enhance (Mo) X-ray Source811 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.031
ω scansθmax = 27.1°, θmin = 3.0°
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2006)
h = 2426
Tmin = 0.827, Tmax = 1.000k = 1111
8068 measured reflectionsl = 58
Refinement top
Refinement on F21 restraint
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.044 w = 1/[σ2(Fo2) + (0.06P)2]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.110(Δ/σ)max < 0.001
S = 1.02Δρmax = 0.32 e Å3
1363 reflectionsΔρmin = 0.19 e Å3
136 parameters
Crystal data top
C13H16O2V = 1136.32 (12) Å3
Mr = 204.26Z = 4
Orthorhombic, Pna21Mo Kα radiation
a = 20.4254 (11) ŵ = 0.08 mm1
b = 8.8913 (6) ÅT = 293 K
c = 6.2570 (4) Å0.3 × 0.05 × 0.03 mm
Data collection top
Oxford Diffraction Xcalibur
diffractometer
1363 independent reflections
Absorption correction: multi-scan
(CrysAlis RED; Oxford Diffraction, 2006)
811 reflections with I > 2σ(I)
Tmin = 0.827, Tmax = 1.000Rint = 0.031
8068 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0441 restraint
wR(F2) = 0.110H-atom parameters constrained
S = 1.02Δρmax = 0.32 e Å3
1363 reflectionsΔρmin = 0.19 e Å3
136 parameters
Special details top

Experimental. The intensity data were collected on a Oxford Xcalibur 3 CCD diffractometer using an exposure time of 20 s/frame. A total of 552 frames were collected with a frame width of 0.5° covering up to θ = 27.09° with 99.9% completeness accomplished. The highest difference peak in the Fourier map is located 0.85 Å from H16.

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C60.60714 (11)0.5148 (3)0.2569 (5)0.0501 (7)
H60.59590.60850.18290.060*
O10.49120 (9)0.4888 (3)0.2890 (4)0.0684 (6)
C20.54437 (13)0.4308 (3)0.3065 (4)0.0522 (7)
C30.64496 (12)0.5550 (3)0.4657 (5)0.0490 (7)
H30.61620.53340.58720.059*
C40.70813 (12)0.4602 (3)0.4926 (5)0.0587 (8)
H4A0.74240.50280.40390.070*
H4B0.72250.46610.64020.070*
C50.69861 (13)0.2986 (4)0.4334 (6)0.0635 (8)
O70.71657 (11)0.1941 (3)0.5432 (5)0.0990 (10)
C80.60166 (13)0.1778 (3)0.2573 (6)0.0609 (8)
H80.61370.09120.34590.073*
C100.64888 (14)0.4191 (3)0.1080 (5)0.0592 (8)
H10A0.68910.47180.07300.071*
H10B0.62530.39950.02360.071*
C110.55214 (12)0.2721 (3)0.3865 (5)0.0571 (8)
H11A0.50990.22260.38210.069*
H11B0.56620.27520.53450.069*
C120.66464 (13)0.2711 (3)0.2209 (5)0.0607 (8)
H120.69420.21290.12940.073*
C150.66318 (14)0.7178 (3)0.4753 (6)0.0652 (9)
H150.68610.75690.35950.078*
C160.5761 (2)0.1174 (5)0.0507 (7)0.0924 (12)
H160.60530.05400.01950.111*
C130.64974 (18)0.8101 (4)0.6321 (7)0.0892 (12)
H13A0.62690.77580.75110.107*
H13B0.66300.91000.62470.107*
C140.5247 (3)0.1352 (5)0.0434 (7)0.1147 (16)
H14A0.49250.19690.01450.138*
H14B0.51750.08720.17340.138*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C60.0477 (14)0.0546 (15)0.0480 (16)0.0009 (13)0.0027 (14)0.0079 (14)
O10.0420 (10)0.1030 (15)0.0603 (12)0.0124 (11)0.0049 (10)0.0058 (11)
C20.0405 (15)0.076 (2)0.0406 (16)0.0009 (13)0.0050 (12)0.0052 (14)
C30.0443 (14)0.0523 (15)0.0504 (16)0.0024 (13)0.0013 (12)0.0010 (14)
C40.0489 (16)0.0657 (18)0.061 (2)0.0011 (14)0.0076 (14)0.0050 (16)
C50.0429 (15)0.067 (2)0.080 (2)0.0088 (15)0.0110 (16)0.0021 (18)
O70.0928 (17)0.0737 (15)0.131 (2)0.0123 (12)0.0493 (19)0.0152 (17)
C80.0605 (17)0.0593 (17)0.0628 (18)0.0035 (14)0.0097 (18)0.0021 (17)
C100.0461 (15)0.081 (2)0.0507 (18)0.0096 (15)0.0074 (14)0.0017 (17)
C110.0464 (15)0.072 (2)0.0531 (16)0.0107 (13)0.0031 (13)0.0032 (16)
C120.0449 (15)0.0669 (18)0.0702 (19)0.0079 (14)0.0060 (15)0.0096 (18)
C150.0522 (16)0.064 (2)0.079 (2)0.0059 (15)0.0006 (16)0.0030 (19)
C160.074 (2)0.115 (3)0.088 (3)0.022 (2)0.005 (3)0.016 (3)
C130.080 (2)0.071 (2)0.116 (3)0.0003 (19)0.017 (2)0.022 (2)
C140.140 (4)0.120 (3)0.084 (3)0.049 (3)0.011 (3)0.002 (3)
Geometric parameters (Å, º) top
C6—C21.516 (4)C8—C121.548 (4)
C6—C101.522 (4)C8—H80.9800
C6—C31.560 (4)C10—C121.528 (4)
C6—H60.9800C10—H10A0.9700
O1—C21.207 (3)C10—H10B0.9700
C2—C111.506 (4)C11—H11A0.9700
C3—C151.496 (4)C11—H11B0.9700
C3—C41.550 (4)C12—H120.9800
C3—H30.9800C15—C131.308 (4)
C4—C51.497 (4)C15—H150.9300
C4—H4A0.9700C16—C141.215 (5)
C4—H4B0.9700C16—H160.9300
C5—O71.212 (4)C13—H13A0.9300
C5—C121.519 (5)C13—H13B0.9300
C8—C161.494 (5)C14—H14A0.9300
C8—C111.543 (4)C14—H14B0.9300
C2—C6—C10108.9 (2)C6—C10—C12108.4 (2)
C2—C6—C3111.1 (2)C6—C10—H10A110.0
C10—C6—C3111.3 (2)C12—C10—H10A110.0
C2—C6—H6108.5C6—C10—H10B110.0
C10—C6—H6108.5C12—C10—H10B110.0
C3—C6—H6108.5H10A—C10—H10B108.4
O1—C2—C11121.7 (2)C2—C11—C8113.8 (2)
O1—C2—C6122.1 (3)C2—C11—H11A108.8
C11—C2—C6116.1 (2)C8—C11—H11A108.8
C15—C3—C4108.3 (2)C2—C11—H11B108.8
C15—C3—C6112.3 (2)C8—C11—H11B108.8
C4—C3—C6112.2 (2)H11A—C11—H11B107.7
C15—C3—H3107.9C5—C12—C10111.3 (2)
C4—C3—H3107.9C5—C12—C8109.7 (3)
C6—C3—H3107.9C10—C12—C8110.8 (2)
C5—C4—C3112.8 (2)C5—C12—H12108.3
C5—C4—H4A109.0C10—C12—H12108.3
C3—C4—H4A109.0C8—C12—H12108.3
C5—C4—H4B109.0C13—C15—C3125.8 (3)
C3—C4—H4B109.0C13—C15—H15117.1
H4A—C4—H4B107.8C3—C15—H15117.1
O7—C5—C4123.8 (3)C14—C16—C8132.4 (4)
O7—C5—C12120.8 (3)C14—C16—H16113.8
C4—C5—C12115.5 (3)C8—C16—H16113.8
C16—C8—C11114.8 (3)C15—C13—H13A120.0
C16—C8—C12110.8 (3)C15—C13—H13B120.0
C11—C8—C12109.3 (2)H13A—C13—H13B120.0
C16—C8—H8107.2C16—C14—H14A120.0
C11—C8—H8107.2C16—C14—H14B120.0
C12—C8—H8107.2H14A—C14—H14B120.0
C10—C6—C2—O1130.0 (3)C16—C8—C11—C279.0 (3)
C3—C6—C2—O1107.1 (3)C12—C8—C11—C246.2 (3)
C10—C6—C2—C1152.1 (3)O7—C5—C12—C10177.9 (3)
C3—C6—C2—C1170.9 (3)C4—C5—C12—C101.6 (3)
C2—C6—C3—C15128.9 (3)O7—C5—C12—C859.1 (4)
C10—C6—C3—C15109.5 (3)C4—C5—C12—C8121.3 (3)
C2—C6—C3—C4108.7 (2)C6—C10—C12—C556.8 (3)
C10—C6—C3—C412.8 (3)C6—C10—C12—C865.5 (3)
C15—C3—C4—C5166.1 (3)C16—C8—C12—C5166.2 (3)
C6—C3—C4—C541.6 (3)C11—C8—C12—C566.2 (3)
C3—C4—C5—O7132.2 (3)C16—C8—C12—C1070.6 (3)
C3—C4—C5—C1248.3 (3)C11—C8—C12—C1057.0 (3)
C2—C6—C10—C1260.4 (3)C4—C3—C15—C13109.0 (3)
C3—C6—C10—C1262.4 (3)C6—C3—C15—C13126.5 (3)
O1—C2—C11—C8136.2 (3)C11—C8—C16—C145.1 (6)
C6—C2—C11—C845.8 (3)C12—C8—C16—C14119.3 (5)

Experimental details

Crystal data
Chemical formulaC13H16O2
Mr204.26
Crystal system, space groupOrthorhombic, Pna21
Temperature (K)293
a, b, c (Å)20.4254 (11), 8.8913 (6), 6.2570 (4)
V3)1136.32 (12)
Z4
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.3 × 0.05 × 0.03
Data collection
DiffractometerOxford Diffraction Xcalibur
diffractometer
Absorption correctionMulti-scan
(CrysAlis RED; Oxford Diffraction, 2006)
Tmin, Tmax0.827, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
8068, 1363, 811
Rint0.031
(sin θ/λ)max1)0.641
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.044, 0.110, 1.02
No. of reflections1363
No. of parameters136
No. of restraints1
H-atom treatmentH-atom parameters constrained
Δρmax, Δρmin (e Å3)0.32, 0.19

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), DIAMOND (Brandenburg, 2000), WinGX (Farrugia, 1999).

 

Acknowledgements

Financial support from the Swedish Research Council, the Knut and Alice Wallenberg Foundation, The Swedish Foundation for Strategic Research, and the Royal Physiographic Society is gratefully acknowledged.

References

First citationAakeröy, C. B. (1997). Acta Cryst. B53, 569–586.  CrossRef Web of Science IUCr Journals Google Scholar
First citationAltomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationBrandenburg, K. (2000). DIAMOND. Crystal Impact GbR, Bonn, Germany.  Google Scholar
First citationDesiraju, G. R. & Steiner, T. (1999). In The Weak Hydrogen Bond. New York: Oxford University Press Inc.  Google Scholar
First citationFarrugia, L. J. (1999). J. Appl. Cryst. 32, 837–838.  CrossRef CAS IUCr Journals Google Scholar
First citationOrentas, E., Bagdziunas, G., Berg, U., Zilinskas, A. & Butkus, E. (2007). Eur. J. Org. Chem. pp. 4251–4256.  Web of Science CrossRef Google Scholar
First citationOxford Diffraction (2006). CrysAlis CCD and CrysAlis RED. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.  Google Scholar
First citationQuast, H., Becker, C., Geibler, E., Knoll, K., Peters, E.-M., Peters, K. & von Schnering, H. G. (1994). Liebigs Ann. Chem. pp. 109–120.  CrossRef Google Scholar
First citationQuast, H., Seefelder, M., Peters, E.-M. & Peters, K. (1999). Eur. J. Org. Chem. pp. 1811–1823.  CrossRef Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWallentin, C.-J., Orentas, E., Johnson, M. T., Butkus, E., Wendt, O. F., Öhrström, L. & Wärnmark, K. (2009). CrystEngComm. Submitted.  Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Follow Acta Cryst. E
Sign up for e-alerts
Follow Acta Cryst. on Twitter
Follow us on facebook
Sign up for RSS feeds